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Merge pull request #237 from nf-core/bracken-params

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Support Kraken and Bracken db_params in database sheet
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James A. Fellows Yates 2023-02-09 10:59:27 +01:00 committed by GitHub
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4 changed files with 61 additions and 13 deletions
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1
conf/modules.config
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@ -355,6 +355,7 @@ process {
withName: BRACKEN_BRACKEN { withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore' errorStrategy = 'ignore'
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
publishDir = [ publishDir = [
path: { "${params.outdir}/bracken/${meta.db_name}/" }, path: { "${params.outdir}/bracken/${meta.db_name}/" },

16
docs/usage.md
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@ -95,7 +95,7 @@ An example database sheet can look as follows, where 5 tools are being used, and
tool,db_name,db_params,db_path tool,db_name,db_params,db_path
malt,malt85,-id 85,/<path>/<to>/malt/testdb-malt/ malt,malt85,-id 85,/<path>/<to>/malt/testdb-malt/
malt,malt95,-id 90,/<path>/<to>/malt/testdb-malt.tar.gz malt,malt95,-id 90,/<path>/<to>/malt/testdb-malt.tar.gz
bracken,db1,,/<path>/<to>/bracken/testdb-bracken.tar.gz bracken,db1,;-r 150,/<path>/<to>/bracken/testdb-bracken.tar.gz
kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
krakenuniq,db3,,/<path>/<to>/krakenuniq/testdb-krakenuniq.tar.gz krakenuniq,db3,,/<path>/<to>/krakenuniq/testdb-krakenuniq.tar.gz
centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz centrifuge,db1,,/<path>/<to>/centrifuge/minigut_cf.tar.gz
@ -103,14 +103,16 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
motus,db_mOTU,,/<path>/<to>/motus/motus_database/ motus,db_mOTU,,/<path>/<to>/motus/motus_database/
``` ```
For Bracken, if you wish to supply any parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty.
Column specifications are as follows: Column specifications are as follows:
| Column | Description | | Column | Description |
| ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `tool` | Taxonomic profiling tool (supported by nf-core/taxprofiler) that the database has been indexed for [required]. Please note that `bracken` also implies running `kraken2` on the same database. | | `tool` | Taxonomic profiling tool (supported by nf-core/taxprofiler) that the database has been indexed for [required]. Please note that `bracken` also implies running `kraken2` on the same database. |
| `db_name` | A unique name per tool for the particular database [required]. Please note that names need to be unique across both `kraken2` and `bracken` as well, even if re-using the same database. | | `db_name` | A unique name per tool for the particular database [required]. Please note that names need to be unique across both `kraken2` and `bracken` as well, even if re-using the same database. |
| `db_params` | Any parameters of the given taxonomic classifier/profiler that you wish to specify that the taxonomic classifier/profiling tool should use when profiling against this specific database. Can be empty to use taxonomic classifier/profiler defaults. Must not be surrounded by quotes [required]. We generally do not recommend specifying parameters here that turn on/off saving of output files or specifying particular file extensions - this should be already addressed via pipeline parameters. | | `db_params` | Any parameters of the given taxonomic classifier/profiler that you wish to specify that the taxonomic classifier/profiling tool should use when profiling against this specific database. Can be empty to use taxonomic classifier/profiler defaults. Must not be surrounded by quotes [required]. We generally do not recommend specifying parameters here that turn on/off saving of output files or specifying particular file extensions - this should be already addressed via pipeline parameters. For Bracken databases, must at a minimum contain a `;` separating Kraken2 from Bracken parameters. |
| `db_path` | Path to the database. Can either be a path to a directory containing the database index files or a `.tar.gz` file which contains the compressed database directory with the same name as the tar archive, minus `.tar.gz` [required]. | | `db_path` | Path to the database. Can either be a path to a directory containing the database index files or a `.tar.gz` file which contains the compressed database directory with the same name as the tar archive, minus `.tar.gz` [required]. |
> 💡 You can also specify the same database directory/file twice (ensuring unique `db_name`s) and specify different parameters for each database to compare the effect of different parameters during classification/profiling. > 💡 You can also specify the same database directory/file twice (ensuring unique `db_name`s) and specify different parameters for each database to compare the effect of different parameters during classification/profiling.

11
subworkflows/local/db_check.nf
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@ -13,8 +13,8 @@ workflow DB_CHECK {
ch_dbs_for_untar = Channel.empty() ch_dbs_for_untar = Channel.empty()
ch_final_dbs = Channel.empty() ch_final_dbs = Channel.empty()
// special check to check _between_ rows, for which we must group rows together // Special check to check _between_ rows, for which we must group rows together
// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first // Note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
Channel.fromPath(dbsheet) Channel.fromPath(dbsheet)
.splitCsv ( header:true, sep:',' ) .splitCsv ( header:true, sep:',' )
.map {[it.tool, it.db_name] } .map {[it.tool, it.db_name] }
@ -25,7 +25,7 @@ workflow DB_CHECK {
if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}" if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}"
} }
// normal checks for within-row validity, so can be moved to separate functions // Normal checks for within-row validity, so can be moved to separate functions
parsed_samplesheet = Channel.fromPath(dbsheet) parsed_samplesheet = Channel.fromPath(dbsheet)
.splitCsv ( header:true, sep:',' ) .splitCsv ( header:true, sep:',' )
.map { .map {
@ -40,7 +40,7 @@ workflow DB_CHECK {
} }
// Filter the channel to untar only those databases for tools that are selected to be run by the user. // Filter the channel to untar only those databases for tools that are selected to be run by the user.
ch_input_untar = ch_dbs_for_untar.untar.dump() ch_input_untar = ch_dbs_for_untar.untar
.filter { .filter {
params["run_${it[0]['tool']}"] params["run_${it[0]['tool']}"]
} }
@ -71,6 +71,9 @@ def validate_db_rows(LinkedHashMap row){
if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}" if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}" if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
// check if any form of bracken params, that it must have `;`
if ( row.tool == 'bracken' && row.db_params && !row.db_params.contains(";") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. Bracken requires a semi-colon if passing parameter. Error in: ${row}"
} }
def create_db_channels(LinkedHashMap row) { def create_db_channels(LinkedHashMap row) {

46
subworkflows/local/profiling.nf
View file

@ -120,8 +120,27 @@ workflow PROFILING {
} }
if ( params.run_kraken2 ) { if ( params.run_kraken2 ) {
// Have to pick first element of db_params if using bracken,
// as db sheet for bracken must have ; sep list to
// distinguish between kraken and bracken parameters
ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "ch_input_for_kraken2_b4")
.map {
meta, reads, db_meta, db ->
def db_meta_new = db_meta.clone()
ch_input_for_kraken2 = ch_input_for_profiling.kraken2 // Only take second element if one exists
def parsed_params = db_meta_new['db_params'].split(";")
if ( parsed_params.size() == 2 ) {
db_meta_new['db_params'] = parsed_params[0]
} else if ( parsed_params.size() == 0 ) {
db_meta_new['db_params'] = ""
} else {
db_meta_new['db_params'] = parsed_params[0]
}
[ meta, reads, db_meta_new, db ]
}
.multiMap { .multiMap {
it -> it ->
reads: [ it[0] + it[2], it[1] ] reads: [ it[0] + it[2], it[1] ]
@ -160,10 +179,33 @@ workflow PROFILING {
.filter { meta, db -> meta['tool'] == 'bracken' } .filter { meta, db -> meta['tool'] == 'bracken' }
.map { meta, db -> [meta['db_name'], meta, db] } .map { meta, db -> [meta['db_name'], meta, db] }
// Extract the database name to combine by. // Combine back with the reads
ch_input_for_bracken = ch_kraken2_output ch_input_for_bracken = ch_kraken2_output
.map { meta, report -> [meta['db_name'], meta, report] } .map { meta, report -> [meta['db_name'], meta, report] }
.combine(ch_bracken_databases, by: 0) .combine(ch_bracken_databases, by: 0)
.map {
key, meta, reads, db_meta, db ->
def db_meta_new = db_meta.clone()
// Have to pick second element if using bracken, as first element
// contains kraken parameters
if ( db_meta['tool'] == 'bracken' ) {
// Only take second element if one exists
def parsed_params = db_meta_new['db_params'].split(";")
if ( parsed_params.size() == 2 ) {
db_meta_new['db_params'] = parsed_params[1]
} else {
db_meta_new['db_params'] = ""
}
} else {
db_meta_new['db_params']
}
[ key, meta, reads, db_meta_new, db ]
}
.multiMap { key, meta, report, db_meta, db -> .multiMap { key, meta, report, db_meta, db ->
report: [meta + db_meta, report] report: [meta + db_meta, report]
db: db db: db